README changes

README.rst

@@ -17,7 +17,7 @@ Installation
 
 Allelic Expression Imbalance
 ============================
-![AEI](doc/source/images/example_aei.png)
+[AEI!](doc/source/images/example_aei.png)
 
 
 Documentation

genda/AEI/AEI.py

@@ -51,6 +51,14 @@ def single_snp_aei_test2(geno, allelic_ratio, num_threshold=2):
         return(ttest_ind(het_combined, homo_combined, equal_var=False)[1])
 
 
+
+
+def single_snp_aei_test_mixture_model(geno, allelic_ration, num_threshold=2):
+
+    pass
+
+
+
 def dosage_round(geno, threshold = 0.5):
     """ Rounds dosage to threshold
     """

genda/stats/popgen.py

@@ -0,0 +1,22 @@
+""" Population Genetic based calculations
+"""
+
+from genda import calculate_minor_allele_frequency
+
+def calculate_D_prime(geno1, geno2):
+    """ Calculates pairwise D_prime of genotype with the
+
+    geno1 - an array or series  
+    geno2 - an array or series
+    """
+    assert len(geno1) == len(geno2)
+    p1 = calculate_minor_allele_frequency(geno1)
+    p2 = calculate_minor_allele_frequency(geno2)
+
+
+    p12 = (geno1 == 2) & (geno2 == 2)
+    p21 = (geno1 == 0) & (geno2 == 0)
+    return(p1 * p2)
+
+
+